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import gradio as gr |
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import cg2all |
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import os |
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def read_mol(molpath): |
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with open(molpath, "r") as fp: |
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lines = fp.readlines() |
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mol = "" |
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for l in lines: |
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mol += l |
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mol = mol.replace("OT1", "O ") |
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mol = mol.replace("OT2", "OXT") |
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return mol |
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def molecule(input_pdb): |
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mol = read_mol(input_pdb) |
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x = ( |
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"""<!DOCTYPE html> |
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<html> |
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<head> |
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<meta http-equiv="content-type" content="text/html; charset=UTF-8" /> |
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<style> |
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body{ |
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font-family:sans-serif |
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} |
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.mol-container { |
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width: 100%; |
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height: 600px; |
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position: relative; |
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} |
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.mol-container select{ |
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background-image:None; |
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} |
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</style> |
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.6.3/jquery.min.js" integrity="sha512-STof4xm1wgkfm7heWqFJVn58Hm3EtS31XFaagaa8VMReCXAkQnJZ+jEy8PCC/iT18dFy95WcExNHFTqLyp72eQ==" crossorigin="anonymous" referrerpolicy="no-referrer"></script> |
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<script src="https://3Dmol.csb.pitt.edu/build/3Dmol-min.js"></script> |
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</head> |
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<body> |
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<div id="container" class="mol-container"></div> |
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<script> |
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let pdb = `""" |
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+ mol |
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+ """` |
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$(document).ready(function () { |
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let element = $("#container"); |
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let config = { backgroundColor: "white" }; |
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let viewer = $3Dmol.createViewer(element, config); |
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viewer.addModel(pdb, "pdb"); |
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viewer.setStyle({}, {cartoon: { color:"spectrum"}}); |
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viewer.addStyle({"and":[{resn:["GLY","PRO"], invert:true}, {atom:["N","C","O"], invert:true}]}, {stick: {radius:0.2, colorscheme:"WhiteCarbon"}}); |
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viewer.addStyle({"and":[{resn:"GLY"}, {atom:"CA"}]}, {stick: {radius:0.2, colorscheme:"WhiteCarbon"}}); |
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viewer.addStyle({"and":[{resn:"PRO"}, {atom:["C","O"], invert:true}]}, {stick: {radius:0.2, colorscheme:"WhiteCarbon"}}); |
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viewer.zoomTo(); |
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viewer.render(); |
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viewer.zoom(0.8, 2000); |
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}) |
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</script> |
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</body></html>""" |
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) |
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return f"""<iframe style="width: 100%; height: 600px" name="result" allow="midi; geolocation; microphone; camera; |
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display-capture; encrypted-media;" sandbox="allow-modals allow-forms |
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allow-scripts allow-same-origin allow-popups |
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allow-top-navigation-by-user-activation allow-downloads" allowfullscreen="" |
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allowpaymentrequest="" frameborder="0" srcdoc='{x}'></iframe>""" |
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def runner(in_pdb, model_type): |
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out_fn = in_pdb.name[:-4] + "-all.pdb" |
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ckpt_fn = f"model/{model_type}.ckpt" |
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cg2all.convert_cg2all(in_pdb.name, out_fn, model_type=model_type, ckpt_fn=ckpt_fn) |
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view = molecule(out_fn) |
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return out_fn, view |
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with gr.Blocks() as app: |
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gr.Markdown( |
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"# cg2all: conversion of coarse-grained protein structure model to all-atom structure" |
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) |
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with gr.Row(): |
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with gr.Column(): |
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input_pdb = gr.File( |
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file_count="single", |
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label="Input CG structure", |
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file_types=[".pdb", ".PDB", ".txt", ".TXT"], |
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) |
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model_type = gr.Radio( |
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[ |
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"CalphaBasedModel", |
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"ResidueBasedModel", |
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"SidechainModel", |
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"CalphaCMModel", |
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"CalphaSCModel", |
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"BackboneModel", |
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"MainchainModel", |
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"Martini", |
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"Martini3", |
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"PRIMO", |
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], |
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label="Input CG model type", |
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) |
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button = gr.Button("Run") |
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gr.Examples( |
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[ |
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["inputs/1ab1_A.calpha.pdb", "CalphaBasedModel"], |
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["inputs/1ab1_A.residue.pdb", "ResidueBasedModel"], |
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["inputs/1ab1_A.sc.pdb", "SidechainModel"], |
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["inputs/1ab1_A.cacm.pdb", "CalphaCMModel"], |
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["inputs/1ab1_A.casc.pdb", "CalphaSCModel"], |
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["inputs/1ab1_A.bb.pdb", "BackboneModel"], |
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["inputs/1ab1_A.mc.pdb", "MainchainModel"], |
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["inputs/1ab1_A.martini.pdb", "Martini"], |
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["inputs/1ab1_A.martini3.pdb", "Martini3"], |
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["inputs/1ab1_A.primo.pdb", "PRIMO"], |
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], |
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[input_pdb, model_type], |
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label="Monomeric coarse-grained structure", |
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) |
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gr.Examples( |
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[ |
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["inputs/Q9EP54.sample.pdb", "CalphaBasedModel"], |
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], |
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[input_pdb, model_type], |
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label="ML(idpGAN)-generated IDP structure", |
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) |
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gr.Examples( |
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[ |
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["inputs/3iyg.pdb", "CalphaBasedModel"], |
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], |
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[input_pdb, model_type], |
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label="Multimeric medium-resolution cryo-EM structure", |
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) |
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gr.Examples( |
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[ |
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["inputs/LAF1rgg.sample.pdb", "CalphaBasedModel"], |
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], |
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[input_pdb, model_type], |
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label="Snapshot of COCOMO simulation of LLPS", |
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) |
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with gr.Column(): |
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output_pdb = gr.File(file_count="single", label="Output structure") |
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viewer = gr.HTML() |
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button.click(fn=runner, inputs=[input_pdb, model_type], outputs=[output_pdb, viewer]) |
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gr.Markdown("---") |
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gr.Markdown( |
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"### GitHub repository: [https://github.com/huhlim/cg2all](https://github.com/huhlim/cg2all)" |
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) |
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gr.Markdown("### Local installation: `pip install git+http://github.com/huhlim/cg2all`") |
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gr.Markdown("### Supported coarse-grained models") |
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gr.Markdown("- CalphaBasedModel: CA-trace") |
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gr.Markdown("- ResidueBasedModel: Residue center-of-mass") |
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gr.Markdown("- SidechainModel: Sidechain center-of-mass") |
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gr.Markdown("- CalphaCMModel: CA-trace + Residue center-of-mass") |
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gr.Markdown("- CalphaSCModel: CA-trace + Sidechain center-of-mass") |
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gr.Markdown("- BackboneModel: Backbone N, CA, and C atoms") |
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gr.Markdown("- MainchainModel: Backbone N, CA, C, and O atoms") |
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gr.Markdown("- Martini: [Martini model](http://cgmartini.nl)") |
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gr.Markdown("- Martini3: [Martini3 model](http://www.cgmartini.nl/index.php/martini-3-0)") |
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gr.Markdown("- PRIMO: [PRIMO model](https://dx.doi.org/10.1002/prot.22645)") |
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gr.Markdown("### Cite: TODO") |
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app.launch() |
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